Seq. Project name:
Sulfurospirillum arcachonense DSM 9755
( Project ID: 1013768 )
Product:
Microbial Minimal Draft, Isolate
Proposal Name:
Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project
(Proposal ID: 733)
Project PI:
User Program:
CSP
Program Year:
2012
Scientific Program:
Microbial
Release Date:
2013-05-31
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Sulfurospirillum / Sulfurospirillum arcachonense / DSM 9755 / |
| GOLD ID: | Gp0013367 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1013768
Sulfurospirillum arcachonense DSM 9755
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 13606504 2x150 Illumina Std PE (cassava 1.8) 6740.1.52790.CCGCAA.fastq
2) ILLUMINA STD PE READ FILTERING STATS:
Reads were screened against synthetic oligos used in the Illumina
sequencing process. Pairs of matching reads were removed from the
dataset.
Total input reads: 13606504 (100%)
Artifact reads removed: 297966 (2.2%)
Total reads removed: 297966 (2.2%)
Total reads remaining: 13308538 (97.8%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 13606504 (100%)
Num contam reads identified: 14 (0.0%)
- Pseudomonas 10 0.00%
- Escherichia 4 0.00%
4) ASSEMBLY STATS:
a) Velvet assembly using VelvetOptimizer:
Assembly stats of the Velvet assembly created by the velvet
optimizer.
Avg GC Content: 31.17 +/- 3.03%
Largest Contig: 324.8 KB
Main genome scaffold total: 52
Main genome contig total: 54
Main genome scaffold sequence total: 2.7 MB
Main genome contig sequence total: 2.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 7/141.2 KB
Main genome contig N/L50: 7/126.3 KB
Number of scaffolds > 50 KB: 20
% main genome in scaffolds > 50 KB: 93.7%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 52 54 2,653,438 2,653,268 99.99%
1 kb 46 48 2,649,124 2,648,954 99.99%
2.5 kb 31 33 2,626,070 2,625,900 99.99%
5 kb 27 29 2,608,620 2,608,450 99.99%
10 kb 24 26 2,589,830 2,589,660 99.99%
25 kb 22 24 2,554,572 2,554,402 99.99%
50 kb 20 22 2,486,725 2,486,575 99.99%
100 kb 11 13 1,875,031 1,874,881 99.99%
250 kb 2 2 588,066 588,066 100.00%
b) Allpaths + Velvet simulated read pairs:
Assembly stats of the ALLPATHS assembly. The input contains simulated
1-3 kb read pairs created from the Velvet assembly and reads that
have been filtered for artifacts.
Avg GC Content: 30.84 +/- 3.26%
Largest Contig: 325.2 KB
Main genome scaffold total: 42
Main genome contig total: 42
Main genome scaffold sequence total: 2.7 MB
Main genome contig sequence total: 2.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 7/141.5 KB
Main genome contig N/L50: 7/141.5 KB
Number of scaffolds > 50 KB: 20
% main genome in scaffolds > 50 KB: 94.0%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 42 42 2,656,384 2,656,374 100.00%
1 kb 42 42 2,656,384 2,656,374 100.00%
2.5 kb 31 31 2,642,010 2,642,000 100.00%
5 kb 27 27 2,624,651 2,624,641 100.00%
10 kb 24 24 2,602,773 2,602,763 100.00%
25 kb 22 22 2,567,453 2,567,443 100.00%
50 kb 20 20 2,497,702 2,497,702 100.00%
100 kb 11 11 1,879,154 1,879,154 100.00%
250 kb 2 2 588,666 588,666 100.00%
5) KEY PIPELINE CMDS:
a) Artifact removal step:
duk params: -k 22 -s 1 -c 1
b) Velvet assembly step for creating simulated read pairs:
Velvet version: 1.1.04
Velvet optimizer version: 2.1.7
Velvet optimizer params: --v --s 51 --e 71 --i 4 --t 1 --f "-shortPaired -fastq $FASTQ" --o "-ins_length 250 -min_contig_lgth 500"
c) Simulated read pairing creation step:
Wgsim version: 0.3.0
Wgsim params: -e 0 -1 100 -2 100 -r 0 -R 0 -X 0
d) ALLPATHS assembly step:
ALLPATHS version: r42328
Contents of in_libs.csv:
library_name, project_name, organism_name, type, paired, frag_size, frag_stddev, insert_size, insert_stddev, read_orientation, genomic_start, genomic_end
STD_1,project,assembly,fragment,1,260,35,,,inward,0,0
SIMREADS,project,assembly,jumping,1,,,3000,300,inward,0,0
6) WORKFLOW STEPS:
1. Removed illumina artifacts (synthetic oligos used in the laboratory).
2. Created velvet assembly of the artifact filtered data.
3. Created simulated 1-3 kb read pairs using Velvet contigs from step 2.
4. Created allpaths assembly using Velvet simulated read pairs (step 3) and the artifact filtered data.
7) ASSEMBLERS USED:
Velvet, AllpathsLG
8) RELEASE DATE:
Mon Apr 22 10:42:41 PDT 2013 By Andrew Tritt- [email protected]
9) AUTHORS:
For additional information, please contact:
Stephan Trong - [email protected]
James Han - [email protected]
This file was automatically generated by the jigsaw pipeline software (version 2.1.2.1).
|
| Funding | |
|---|---|
| The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. | |
| Groups |
|---|
| ## | Name | Type |
|---|---|---|
| 1 | Environmental | |
| 2 | Epsilonproteobacteria |
